Bland-Altman plot, R code.

baplot.R

# Bland-Altman plot R function.
# Author: jmmateos@mce.hggm.es
baplot <- function(m1, m2, ...) {
    # m1 and m2 are the measurements
    means <- (m1 + m2) / 2
    diffs <- m1 - m2
    mdiff <- mean(diffs)
    sddiff <- sd(diffs)
    
    # Compute the figure limits
    ylimh <- mdiff + 3 * sddiff
    yliml <- mdiff - 3 * sddiff
    
    # Plot data
    plot(diffs ~ means, xlab = "Average values", 
         ylab = "Differences", ylim = c(yliml, ylimh), ...)    
    abline(h = mdiff) # Center line
    # Standard deviations lines
    abline(h = mdiff + 1.96 * sddiff, lty = 2)
    abline(h = mdiff - 1.96 * sddiff, lty = 2)
}